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Calcium in PDB 7vpf: Crystal Structure of A Novel Putative Sugar Isomerase From the Psychrophilic Bacterium Paenibacillus Sp. R4

Protein crystallography data

The structure of Crystal Structure of A Novel Putative Sugar Isomerase From the Psychrophilic Bacterium Paenibacillus Sp. R4, PDB code: 7vpf was solved by H.H.Park, J.H.Lee, S.Kwon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.82 / 2.98
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 141.932, 141.932, 76.701, 90, 90, 120
R / Rfree (%) 21.4 / 27.1

Other elements in 7vpf:

The structure of Crystal Structure of A Novel Putative Sugar Isomerase From the Psychrophilic Bacterium Paenibacillus Sp. R4 also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of A Novel Putative Sugar Isomerase From the Psychrophilic Bacterium Paenibacillus Sp. R4 (pdb code 7vpf). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of A Novel Putative Sugar Isomerase From the Psychrophilic Bacterium Paenibacillus Sp. R4, PDB code: 7vpf:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7vpf

Go back to Calcium Binding Sites List in 7vpf
Calcium binding site 1 out of 2 in the Crystal Structure of A Novel Putative Sugar Isomerase From the Psychrophilic Bacterium Paenibacillus Sp. R4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of A Novel Putative Sugar Isomerase From the Psychrophilic Bacterium Paenibacillus Sp. R4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:126.7
occ:1.00
OE2 A:GLU247 2.4 119.1 1.0
OE1 A:GLU247 2.4 128.8 1.0
CD A:GLU247 2.7 110.0 1.0
CE1 A:HIS203 3.0 105.3 1.0
OE2 A:GLU142 3.3 90.7 1.0
ND1 A:HIS203 3.4 116.2 1.0
SG A:CYS67 3.6 105.8 1.0
ZN A:ZN302 3.8 200.5 1.0
OE1 A:GLU142 3.8 114.7 1.0
CD A:GLU142 3.9 93.7 1.0
ND2 A:ASN13 3.9 79.8 1.0
NE2 A:HIS203 4.1 76.1 1.0
CG A:GLU247 4.1 97.7 1.0
CG1 A:VAL103 4.5 65.6 1.0
CG A:HIS203 4.6 86.0 1.0
CB A:CYS67 4.7 72.2 1.0
CB A:GLU247 4.7 95.1 1.0
OE2 A:GLU245 4.8 95.9 1.0
CG A:ASN13 4.8 84.6 1.0
CZ2 A:TRP40 4.9 82.0 1.0
CD2 A:HIS203 4.9 74.4 1.0
CG2 A:VAL103 5.0 83.3 1.0
OD1 A:ASN13 5.0 73.2 1.0

Calcium binding site 2 out of 2 in 7vpf

Go back to Calcium Binding Sites List in 7vpf
Calcium binding site 2 out of 2 in the Crystal Structure of A Novel Putative Sugar Isomerase From the Psychrophilic Bacterium Paenibacillus Sp. R4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of A Novel Putative Sugar Isomerase From the Psychrophilic Bacterium Paenibacillus Sp. R4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca302

b:133.5
occ:1.00
OE2 B:GLU247 2.4 119.2 1.0
OE1 B:GLU247 2.5 115.5 1.0
CD B:GLU247 2.8 107.1 1.0
OE2 B:GLU142 2.8 99.3 1.0
ZN B:ZN301 2.9 175.0 1.0
CE1 B:HIS203 3.2 102.9 1.0
ND1 B:HIS203 3.5 99.1 1.0
SG B:CYS67 3.7 98.3 1.0
CD B:GLU142 3.8 101.4 1.0
OE1 B:GLU142 4.0 125.5 1.0
CG B:GLU247 4.3 94.7 1.0
CG1 B:VAL103 4.4 64.3 1.0
ND2 B:ASN13 4.4 81.0 1.0
NE2 B:HIS203 4.5 84.2 1.0
CZ2 B:TRP40 4.8 89.2 1.0
CG B:HIS203 4.8 84.2 1.0
CB B:GLU247 4.9 93.8 1.0

Reference:

S.Kwon, H.J.Ha, Y.J.Kang, J.H.Sung, J.Hwang, M.J.Lee, J.H.Lee, H.H.Park. Crystal Structure of A Novel Putative Sugar Isomerase From the Psychrophilic Bacterium Paenibacillus Sp. R4. Biochem.Biophys.Res.Commun. V. 585 48 2021.
ISSN: ESSN 1090-2104
PubMed: 34784551
DOI: 10.1016/J.BBRC.2021.11.026
Page generated: Wed Mar 30 13:59:06 2022

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